Light in the Darkness
by Charmeleon2012
Summary: When the glitch Pokemon, Missigno, returns to attempt to restore its power and overthrow the legendary Pokemon, it's up to the Sinnoh Champion, Cynthia, and her mentor, Dawn, to stop him. But will the secrets of the past and future hinder them in their fight to restore order to their world?
1. Chapter 1

**Author's Note: Hey guys! In case you haven't noticed, I'm new here and this is my first attempt at writing a story, so please be gentle. Honestly, this idea just popped into my head recently, so I decided to type it up and try and make it into something. I should warn you, I do have restricted computer access because of reasons, so updating may be a little slow. Please be patient; between minimal time to type up these stories I also have bouts of depression at times, meaning I lose my motivation to work. I also have about ten different stories in my head right now so I might lose track of things. For now, please try to stay with me, and I'll do the best I can. My main goal here is to keep track of and improve my writing skills, so reviews would definitely be great 3**

**I should also inform you that this fic will most likely contain yuri (Girlpowershipping) and an eight-year age gap. If this offends you in any way, you might as well leave now. Otherwise, enjoy :)**

**((Rated T for above reasons, plus some language and possible violence in future chapters))**

The library was dimly lit, save a few ghostly blue flames which flickered on and off as they pleased. An old lantern housing a deep purple flame was also situated over the desk, the only pieces of furniture in the room besides the huge bookshelves. These shelves stretched endlessly throughout every crevice in the room, touching the ceiling and disappearing far below the middle platform, which was also littered with books and papers. One of the only living souls within the room was a tall, silver-eyed woman wearing dark- colored clothing, with golden blonde hair that completely covered her one eye and fell all the way to the back of her knees. She also had a pair of bright red spectacles perched on her nose, though they were much too big for her and kept threatening to slip off. The other was a blue wolflike creature, who was currently standing on the tip of his toes in order to shovel books off the higher shelves and into his own arms. Both were on the same mission; to collect as many useful books as they possibly could.

Cynthia squinted in the dim light as she reached for a particular book, a thick, leather-bound one with golden lettering printed on the side. Carefully, she tucked it in the crook of her arm and climbed down from the ladder she was perched on. As she reached the ground, she was greeted by her companion, Lucario, who was struggling to balance his own load of books. Cynthia took the heavy stack into her own arms, and the Pokémon sighed in relief.

"That will be all for now. Thank you, Lucario."

_Yes, Master. _ He wandered off, only to plop down onto a large stack of books, fumbling with the pages of a novel nearest him and muttering something in his head about slave workers.

"No need to be formal, dear," Cynthia hummed. She had already put her own books down on the desk and was hastily pulling more off the shelves. "No need to be sarcastic, either," she added bemusedly.

_Well, in case you haven't noticed, I'm not exactly in perfect form right now. _He stretched out his arms, wincing when something finally cracked. _Don't you have that old dinosaur around to do the heavy work for you?_

"Oh, hush, Lucario. You know she's in worse shape than you right now." Indeed, the "old dinosaur", Cynthia's Garchomp, _was _in rather rough shape due to a recent battle with yet another trainer aspiring to become the new Champion. Cynthia beat him easily, of course, but his surprising attack combinations came in such quick succession that it made her poor darling Pokémon's head spin. Regrettably, she hadn't had the time to take Garchomp or anyone else to a Pokémon Center, so she finally decided on leaving her home to rest. Unfortunately, the blonde needed _someone _to help her with finding her books on the shelves, and Lucario was her only other partner she trusted with handling them. "You know," she said, turning to him as she grinned, "if I were you, I would be thrilled to be my second favorite." Lucario snorted in response and grabbed the book he'd been toying with, flipping to the cover page and pretending to become engrossed in his reading. Cynthia rolled her eyes and returned to the bookshelves, quickly becoming reabsorbed in her task.

Cynthia was just returning to the desk with another armful of precious books when a loud bang sounded right behind her. Startled, the Champion dropped the novels in her hands, nearly crushing her foot with a particularly large hardcover. She whirled around angrily, preparing to scold her Pokémon for being so careless, but instead squealed girlishly as she came face-to-face with a dark, slightly shorter but just as intimidating figure. It was a woman, with short-cropped hair and a purple-schemed outfit that was quite a few shades darker than her hair. A huge deep violet bow stuck out behind her neck, and the glasses she wore matched those that now sat precariously on Cynthia's nose. Despite the irritating darkness of the library, Cynthia recognized the woman immediately. She groaned and spun around dramatically, bending over to pick up what she'd dropped.

"Goddamnit, Shaun," the blonde whined as she worked to retrieve the books, "how many times do I have to tell you to knock?"

"None." The Elite Four member, Shauntal, stepped forward. "This is _my _library, Cindy."

Cynthia, meantime, had returned to Shauntal's desk. "Oh, please. You and I both know we have better things to worry about than whose library this is." The writer waved off the Champion's words.

"That doesn't give you the right to break in here and use my belongings whenever you please." She pinched the bridge of her nose, which she often did when she was stressed. "I suppose those are my spectacles you're wearing, aren't they?"

"No, these are mine."

"That's not true. You don't have your own reading glasses."

"Actually, I just bought some a few days ago." Cynthia rolled the ladder over to another section of the library, stretching as she reached for the spine of a book on the top shelf. "I had them with me, but they were too small and I accidentally dropped them off the platform anyway, so I borrowed some of yours." The Champion's voice dropped steadily as she confessed, even though she knew the older woman could care less. Shauntal could only watch in mild concern as the blonde pored over the huge collection of books she had impulsively collected. Finally, she sighed and shook her head.

"Cynthia…. You do know you can't get all the answers from books, right? I believe I've told you before, and I'm not wrong, that books are fountains of knowledge, but when it comes to these kinds of situations, the well tends to run dry. This is all very stressful for you, and I know you'd like to think that you can solve your problems just by reading yourself out of them, but you can't always rely on the words of others to help you. Sometimes you have to pay attention to what's written between the lines before you can find your true answer. Does that make sense?"

Cynthia was silent for a long time. Shauntal told her this every time she caught the Champion in her library, and the blonde believed her, she did. It was always a compulsive decision to come here and dig through mountains of books just to learn everything she already knew. Even her Pokémon questioned it, but she couldn't seem to stop herself from turning to the library for answers. It was no longer a simple quest for general information, or to bug Shauntal. Cynthia wanted real answers, better answers, anything that would explain to her exactly what she was supposed to do. Nothing she found could tell her this, though, and so she continued to hoard the same books over and over again, skipping trivial sections and turning straight to the facts. They were great facts, sure, but nothing more than that. Nothing could tell her how to handle this situation, and not knowing was perhaps the only thing the Champion truly feared.

Cynthia spent a whole minute staring blankly at the open book in front of her before promptly slamming her head down on the desk.

"Shit." She lifted her head up, carefully pushing blonde tresses from her one eye. The other, she preferred to keep hidden under golden locks. "Are you sure he's coming back, so soon? Nothing in the books says he's allowed to come early."

"I don't think he needs permission, Cynthia."Shauntal stepped forward and put a comforting hand on the younger woman's shoulder. "I suppose your own role in this isn't all you're worried about, is it?"

This time, Cynthia buried her face in her hands. "She's not ready, Shauntal."

The writer nodded. "I thought so. I think you've done a good job training her."

"It doesn't matter if she's not ready, now does it?"

"How do you know she isn't ready? Have you even told her about the Prophecy yet?"

"No, and I don't plan to."

Shauntal sighed. "If you won't, then someone else will. Alder. Johanna. I might even do it myself. Do you really want it to come to that?"

The blonde glared at her, her gray eyes flashing. "No. No, I don't." Her expression softened a little. "I just don't want to scare her away…" Cynthia became cold again when she noticed the older woman giving her an amused look. "What? Why are you looking at me like that?"

Shauntal chuckled. "'I've never seen you care so much about anyone besides your own Pokémon. Is the great Sinnoh Champion Cynthia perhaps going soft?" She laughed again when Cynthia shoved her.

"Shut up, Shaun. I care about plenty of people. Just not for you." Shauntal was about to reply when she felt the ground shift beneath her. Every wandering flame in the room flickered. Books rattled on the shelves as a deep rumble resonated throughout the hall. Lucario, who by this time had fallen asleep, jerked awake and leapt up to catch the rolling ladder just before it fell squarely on his head. The two women, along with Cofagrigus, whom Shauntal had just summoned, were busy catching stray books that dropped from the rattling shelves. When the tremors finally ceased, the room appeared to be unaffected, save the mess of books and papers now scattered among the floor. The mysterious blue flames, which had sputtered out just as the tremors began, reappeared and scattered themselves throughout the room, clumsily trying to pick up loose papers in order to replace them on the desk. Cynthia watched all this with a grave intensity before her gaze drifted to her hand as it was pressed agitatedly to her forehead.

"You were right," she said quietly.

"Wasn't I?" Shauntal mused, more to herself than to the younger woman. She surveyed the hall for any damages, frowning whenever she came upon a cracked shelf or a gap between her endless collections of books. Her Pokémon was currently busy helping the small army of ghost flames reshelf the books which had fallen. The writer turned to Cynthia. "There doesn't seem to be too much damage," she said matter-of-factly. "That tremor has been the worst one yet, though."

"You mean there have been other tremors?" The Champion asked, surprised.

"Yes. You haven't noticed?" Cynthia shook her head. "No, of course you haven't. They've all happened at night, and I know how you sleep as soundly as a dead Magikarp." The blonde made a face, but Shauntal waved it off. "Anyway, there have been three more previously, each one more powerful than the last."

"Has anyone else noticed?"

I haven't asked anyone else yet, but I'm sure N's noticed. He can speak to Pokémon, after all, so he's already talked to him, I assume. Of course nobody would expect him to listen to reason. He'll come, no matter what anyone says." Cynthia blinked, her emotions spinning in useless circles within her mind. She had the strong urge to run away and find a place to hide, taking the destiny-bound girl with her in order to somehow protect her from the inevitable. Her task was dangerous, and the prophecy didn't say anything about whether or not she would be ready if he came early. Putting the girl in danger was the last thing the Champion wanted to do.

_Shaun's right, I really am going soft…. _Cynthia thought miserably, rubbing her throbbing temples.

The writer noticed the blonde's sudden downcast expression and stepped forward to put a comforting hand on her shoulder. "Look, I know you only want what's best for her," she said quietly, "but she has to do this. Nothing can change her path, not even you. You know that, right?" The younger woman nodded stiffly, and then swiped at her eyes, which had begun to brim with tears, with her coat sleeve. The older woman smiled and patted her cheek. "Good girl." She stood tall in front of Cynthia and offered her a confident smile.

"Now, then, you should get going. Missigno is returning, and you need to go make sure Dawn is ready for him."


	2. Chapter 2

**Author's Note: Hey guys, it's me again :D Sorry to keep you waiting, I'm trying my best to update when I can, but I finally got the time to type up the next chapter! Yee! Oh, and I'm not sure if I've mentioned this before but I honestly have almost no idea where this story is going…. But hey, I'm gonna try as hard as I can, so anyone who wants to come along for the ride is certainly welcome. I'm also writing this chapter by the Pokémon Black Version storyline; that is, the player was accepted by Reshiram, whereas N was recognized by Zekrom. Also, I used the Black2/White2 ex-Team Plasma hideout. I hope that doesn't bother anyone : Reviews are nice though; I'd especially like to know if these chapter lengths are working out for everyone, or if they should be longer/shorter. Don't be afraid to tell me :) Oh yeah, and in case you haven't noticed, sentences in **_**italics **_**are a character's thoughts. But you probably knew that, because you're smart c: ANYWHO, let's get on with the story, shall we?**

**Disclaimer: I do not own Pokémon or Nintendo.**

N sat back in his desk chair, lost in his own thoughts. Having long since given up his dream (or rather, Ghetsis' dream) of liberating Pokémon from people, he had more time to spend with the legendary Pokémon, Zekrom, who had happened to choose him, of all people, as the hero. He never fully understood what made him so special, other than the fact that he could talk to Pokémon, and honestly he'd never cared enough to ask. N was content just being with Zekrom as they travelled the world together, hardly speaking except for on rare occasions when the Pokémon would find something interesting and point it out to him. For now, though, their journey had been momentarily delayed. Both N and Zekrom had sensed that something powerful and unfriendly had gathered itself within their home region, a matter that seemed much more urgent to them then their silent travels.

_Give me Light._

N sensed the tremor coming before he even felt the ground start to shake beneath him.

"Tremor!" He called out into the echoing halls of the building which housed many of Team Plasma's former members. Rood, who was sitting on his overstuffed chair and reading the newspaper, sat up suddenly, his head jerking from side to side. Everyone else in the room, including N, dropped onto the ground just as the most powerful quake yet shook the whole room. Some of the Pokémon, who were scuttling about in fear and confusion, lost their footing and fell hard on the tiled floor. A young Patrat crawled over to N and cowered in his lap.

As the room finally stopped shaking, everyone on the floor got up slowly. Rood, who had flopped off his chair onto the floor sometime during the quake, grumbled loudly as he struggled to push himself up. N's caretakers, who still saw him as a young, helpless boy even though he was quite grown up, came over to him and pulled him to his feet, checking him for any damages.

"Hey, I'm fine. Don't worry about me. Could you please go check on the Pokémon that fell?" They nodded hesitantly, giving him one last assessing glance before busying themselves with plucking fallen Pokémon off the floor. All of them seemed dazed and somewhat bruised, but otherwise unhurt.

N, on the other hand, was very distressed. That tremor had been the worst one yet, filled with more power and rage than ever before. He didn't know exactly where Missigno was drawing all his power from, and not knowing made him very nervous.

_Master N! _A soft but firm voice rang clearly in his head, and he turned in the direction it was coming from. There, squatting at the front door of the building, sat a large Caterpie, looking straight into N's eyes and mirroring his concern. N blinked, and then smiled at the new arrival.

"Captain Orion, I presume," the young man said, kneeling down next to the Bug Pokémon. "It's a pleasure to see you again. How are things back home?"

_Oh, very well, my lord. The fierce leader of the Fearow Legion, Bastion, has sent many gifts to us from his kingdom in order to make amends for his former behavior. _The Caterpie's voice was very low and rugged, a feature that most people would find comical. N, however, had not once cracked a smile at this idea, for he knew the Pokémon was a great leader and warrior despite his size, and laughing at him would certainly hurt his pride. Instead, N extended a hand towards the creature, who gratefully crawled up his arm and perched on the boy's shoulder. He walked over to his desk and sat down, placing Orion next to the open book that N had previously been studying. He'd expected Orion to immediately begin talking about the recent alliance with the Fearow Legion, and how, after years of quarrels and territorial disputes, the two clans had learned to live together and share the forest equally, with a little help from N and Zekrom. He was surprised when the Caterpie remained silent, carefully studying the book in front of him before looking up and locking eyes with the green-haired boy.

_Lord N, I'm afraid I have grave news, _Orion told him, his thoughts quiet and dark. N nodded. He was afraid of that.

_Missigno is living in Pinwheel Forest._

N startled, dropping the pen in his hand and flinching as it clattered to the floor. "That's impossible," he said, turning to the front door as it creaked open and a black nose nuzzled its way inside. Zekrom must have heard his thoughts, because he was now looking directly at the pair, a concerned look on his face.

_It's true! _Orion insisted. _He is recruiting Pokémon there, hypnotizing them into doing his bidding. He tells them that it isn't fair to our race that the humans have control over us. He sends his followers to raid human cities and towns during the night and steal food and other things. Missigno is deliberately trying to cause panic and chaos, but I also think there is another reason behind all this._

_Of course there is, _a powerful yet nervous voice rang through both N's and Orion's minds, making them both jump in surprise. It was Zekrom. _Missigno is searching for the one item that will restore him to power: The Light Orb._

_He is a fool, then, _the Caterpie chided. _That Orb was removed from the Temple of Elements and destroyed by Arceus himself._

_So the legends say. However, if the Orb _had_ been_ _completely destroyed, Missigno would not have as much power as he does today, right now. There must have been some mistake; somehow the Orb, or at least a fraction of it, has been salvaged._

"That's why the Prophecy was written," N chimed in. Everything was starting to click together like a puzzle in his mind, and he did not like the dark, sinister scene that this particular puzzle portrayed. Zekrom nodded, his chin coming down rather hard onto the floor as he settled, and the building shook slightly due to the sudden upset. The legendary Pokémon cursed silently, then continued.

_Someone obviously knew that the Orb was still useable, or else the Prophecy would have never been written. Whether it was Arceus or not, they were foolish not to seek and destroy the remaining pieces of the Orb immediately. _Zekrom turned as best he could to face Orion. _Tell me, what form had Missigno taken when you last saw him?_

_A human, _the Caterpie replied after a moment's pause. _But he could speak easily to Pokémon, and they listened to him despite his appearance._

_He has gained more power than I thought, then. I assume he is also using a strong charm or spell of some kind in order to keep himself hidden from the Legendary Pokémon. I highly doubt we will be able to find him, even if we tried._

"Well, we can't just sit around waiting for him to come to us!" N fumed, and Orion nodded in wholehearted agreement.

_I am afraid we do not have a choice._

N sighed. Zekrom was right. Even if they did find Missigno, what could they do? This wasn't their battle. According to the Prophecy, Missigno could only be stopped by the legendary Sword of Justice, the powerful weapon that the Swords of Justice represented and were bound to protect. Not only that, but the Sword could only be wielded by one person, the one chosen by the Prophecy. Speaking of whom…

"Dawn." N had forgotten all about the young prodigy, considering it wasn't his job to be training her. Even so, knowinghow overprotective her mentor, Cynthia, really was when it came to the girl, he was almost positive Dawn was still blissfully unaware of the task she was bound to complete. If what Zekrom said was true, if Missigno really was using the Light Orb to regain power faster than ever before, then he had to make sure that she started her training right away. Otherwise, the final chapter of the Prophecy may be written in Dawn's blood. "Zekrom, we have to go to Undella Town right away." The Pokémon nodded, for he had already sensed his master's thoughts.

_Cynthia will not be pleased, _he noted.

"I don't care. We're leaving, now." As he said this, he finished scribbling down a note to Rood and his caretakers about his plans, only so they wouldn't worry about him and try to find him.

_I am coming, too,_ Orion spoke up. _It will be an honor to serve my lord N in his quest to restore order to the world. _N was hesitant at first, but finally he nodded.

"Okay." He picked the Pokémon up off the desk without another word and carried him to the front entrance. Zekrom had already backed out of the doorway so that N could get through and climb up onto the Pokémon's back. With Orion sitting back up on his shoulder, gripping tightly so as not to fall off during takeoff, the boy tapped Zekrom's shoulder, urging him to fly upwards. He complied easily, spreading his wings as his generator-like tail whirred and snapped. A powerful burst of lightning struck the ground, propelling the Pokémon and his passengers skyward. N held tightly onto his hat as a powerful gust of wind hit him square in the face.

Once in the air, Zekrom slowed, tilting his body farther sideways. N relaxed, letting go of his hat and looking over to see if Orion was still there. He was, and his large eyes crinkled into a smile. N smiled back, patting his larger companion's neck and preparing himself for a long, smooth ride.

None of them noticed a sinister pair of glowing red eyes glaring at them as the trio passed over the Pinwheel Forest canopy.


End file.
